15-101267710-T-C

Variant names:

• chr15-101267710-T-C
• rs2101171

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.192 in 152,202 control chromosomes in the GnomAD database, including 3,647 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29217 AN: 152086 Hom.: 3646 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.185

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.192 AC: 29221 AN: 152202 Hom.: 3647 Cov.: 32 AF XY: 0.194 AC XY: 14440 AN XY: 74402

African (AFR) AF: 0.0457 AC: 1901 AN: 41568

American (AMR) AF: 0.196 AC: 2991 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3466

East Asian (EAS) AF: 0.169 AC: 873 AN: 5168

South Asian (SAS) AF: 0.171 AC: 823 AN: 4820

European-Finnish (FIN) AF: 0.323 AC: 3417 AN: 10578

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17527 AN: 67996

Other (OTH) AF: 0.183 AC: 386 AN: 2114

Alfa AF: 0.226 Hom.: 7088

Bravo AF: 0.178

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.74
PhyloP100		-0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2101171; hg19: chr15-101807915;